Make system todo list

* Add logging of hidden commands
* Change dependency system to create .d when creating .o
* Change dependencies so that deps directories are only created for a .o target

- Test make system using windows gnu make and using cygwin
- Test make system using extended debug symbols and netbeans
    CFLAGS="-g3 -gdwarf-2" CXXFLAGS="-g3 -gdwarf-2"

- Add `run' targets to make system
- Add compile environment echo commands to make system (ex. echo-includes)